miRNA: 3'- cCCGGU--UCU---UGUCU---ACCAGgGGUCUa -5'
miRNA: 3'- -CCCGGUUCUUgUCU------------ACCAGGGG-UCUA- -5'
miRNA: 3'- -CCCGGUUCUUGUCUACCagggGUCua -5'
miRNA: 3'- -CCCGGUUCUUGUCUACCAGGGGUCUA- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 3181 | 5' | -55.1 | NC_001501.1 | + | 5730 | 0.67 | 0.162305 |
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Target: 5'- aGGCCAccAGGuccACAGAgggUGGUUgCCAGAa -3' miRNA: 3'- cCCGGU--UCU---UGUCU---ACCAGgGGUCUa -5' |
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| 3181 | 5' | -55.1 | NC_001501.1 | + | 1969 | 0.68 | 0.125348 |
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Target: 5'- aGGGUCAGGAG-GGAggucuggggucuUGGUCCCCgAGGUc -3' miRNA: 3'- -CCCGGUUCUUgUCU------------ACCAGGGG-UCUA- -5' |
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| 3181 | 5' | -55.1 | NC_001501.1 | + | 7719 | 0.73 | 0.056276 |
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Target: 5'- aGGGCCAAGAACAGAUGGaa--CAGc- -3' miRNA: 3'- -CCCGGUUCUUGUCUACCagggGUCua -5' |
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| 3181 | 5' | -55.1 | NC_001501.1 | + | 7794 | 1.09 | 6e-05 |
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Target: 5'- aGGGCCAAGAACAGAUGGUCCCCAGAUg -3' miRNA: 3'- -CCCGGUUCUUGUCUACCAGGGGUCUA- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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